Sample Resequencing Stats

Note: The mutation counts shown below represent unfiltered mutation sets.
ALE, Flask, Isolate Predicted Mutations Mean Coverage Total Reads Percent Mapped Mapped Reads Average Read Length
A1 F2 I198 R1 96 36.2 2313912 84.6% 1957569 85.2

Breseq alignment

N/A

GATK/CNVnator alignment

BRESEQ :: bam2aln output
TGAAACTCCTGCGAGAACGTGCCGTGCTGTAATAACAGGATGCGGTCACACACCAGCGGCAACTCCTCCACTTCACTGGAGATAAACACCACGCTTTTTCCTTCGGCAGCCAGCTCACGGACAATACGGTAAATCTGCTGTTTGGCTTCGATATCGACGCCGCGCGTTGGCTCGTCGAGCAACAAAATCTGGC  >  NZ_CP009273/2670261‑2670453
                                                                                                  |                                                                                              
taagagacagGCGAGAACGTGCCGTGCTGTAATAACAGGATGCGGTCACACACCAGCGGCAACTCCTCCACTTCACTGGAGATAAACACCACGCTTTTCC                                                                                               <  SRR3722077.369910/90‑1 (MQ=60)
             AGAACGTGCCGTGCTGTAATAACAGGATGCGGTCACACACCAGCGGCAACTCCTCCACTTCACTGGAGATAAACACCACGCTTTTTCCTTCGGCAGCCAG                                                                                  >  SRR3722077.719561/1‑100 (MQ=60)
             AGAACGTGCCGTGCTGTAATAACAGGATGCGGTCACACACCAGCGGCAACTCCTCCACTTCACTGGAGATAAACACCACGCTTTTCCCTTCGGCAGCCAG                                                                                  >  SRR3722077.495697/1‑100 (MQ=60)
                           TGTAATAACAGGATGCGGTCACACACCAGCGGCAACTCCTCCACTTCACTGGAGATAAACACCACGCTTTTCCCTTCGGCAGCCAGCTCACGGACAATAC                                                                    <  SRR3722077.236548/100‑1 (MQ=60)
                            GTAATAACAGGATGCGGTCACACACCAGCGGCAACTCCTCCACTTCACTGGAGATAAACACCACGCTTTTTCCTTCGGCAGCCAGCTCACGGACAATACG                                                                   >  SRR3722077.92595/1‑100 (MQ=60)
                            GTAATAACAGGATGCGGTCACACACCAGCGGCAACTCCTCCACTTCACTGGAGATAAACACCACGCTTTTTCCTTCGGCAGCCAGCTCACGGACAATACG                                                                   >  SRR3722077.104762/1‑100 (MQ=60)
                              AATAACAGGATGCGGTCACACACCAGCGGCAACTCCTCCACTTCACTGGAGATAAACACCACGCTTTTTCCTTCGGCAGCCAGCTCACGGACAATACGGT                                                                 <  SRR3722077.787096/100‑1 (MQ=60)
                              AATAACAGGATGCGGTCACACACCAGCGGCAACTCCTCCACTTCACTGGAGATAAACACCACGCTTTTTCCTTCGGCAGCCAGCTCACGGACAATACGGT                                                                 <  SRR3722077.470073/100‑1 (MQ=60)
                              AATAACAGGATGCGGTCACACACCAGCGGCAACTCCTCCACTTCACTGGAGATAAACACCACGCTTTTCCCTTCGGCAGCCAGCTCACGGACAATACGGT                                                                 <  SRR3722077.184060/100‑1 (MQ=60)
                              AATAACAGGATGCGGTCACACACCAGCGGCAACTCCTCCACTTCACTGGAGATAAACACCACGCTTTTCCCTTCGGCAGCCAGCTCACGGACAATACGGT                                                                 <  SRR3722077.201498/100‑1 (MQ=60)
                              AATAACAGGATGCGGTCACACACCAGCGGCAACTCCTCCACTTCACTGGAGATAAACACCACGCTTTTCCCTTCGGCAGCCAGCTCACGGACAATACGGT                                                                 >  SRR3722077.295531/1‑100 (MQ=60)
                                   CAGGATGCGGTCACACACCAGCGGCAACTCCTCCACTTCACTGGAGATAAACACCACGCTTTTCCCTTCGGCAGCCAGCTCACGGACAATACGGTAAATC                                                            <  SRR3722077.105986/100‑1 (MQ=60)
                                           GGTCACACACCAGCGGCAACTCCTCCACTTCACTGGAGATAAACACCACGCTTTTCCCTTCGGCAGCCAGCTCACGGACAATACGGTAAATCTGCTGTTT                                                    <  SRR3722077.192184/100‑1 (MQ=60)
                                            GTCACACACCAGCGGCAACTCCTCCACTTCACTGGAGATAAACACCACGCTTTTCCCTTCGGCAGCCAGCTCACGGACAATACGGTAActgtctcttata                                                   >  SRR3722077.945566/1‑88 (MQ=60)
                                                CACACCAGCGGCAACTCCTCCACTTCACTGGAGATAAACACCACGCTTTTCCCTTCGGCAGCCAGCTCACGGACAATACGGTAAATCTGCTGTTTGGCTT                                               >  SRR3722077.374237/1‑100 (MQ=60)
                                                          GCAACTCCTCCACTTCACTGGAGATAAACACCACGCTTTTTCCTTCGGCAGCCAGCTCACGGACAATACGGTAAATCTGCTGTTTGGCTTCGATATCGAC                                     <  SRR3722077.945721/100‑1 (MQ=60)
                                                             ACTCCTCCACTTCACTGGAGATAAACACCACGCTTTTTCCTTCGGCAGCCAGCTCACGGACAATACGGCAAATCTGCTGTTTGGCTTCGATATCGACGCC                                  >  SRR3722077.834061/1‑100 (MQ=60)
                                                                CCTCCACTTCACTGGAGATAAACACCACGCTTTTTCCTTCGGCAGCCAGCTCACGGACAATACGGTAAATCTGCTGTTTGGCTTCGATATCGACGCCGCG                               >  SRR3722077.417870/1‑100 (MQ=60)
                                                                             GGAGATAAACACCACGCTTTTTCCTTCGGCAGCCAGCTCACGGACAATACGGTAAATCTGCTGTTTGGCTTCGATATCGACGCCGCGCGTTGGCTCGTCG                  >  SRR3722077.349144/1‑100 (MQ=60)
                                                                                            GCTTTTCCCTTCGGCAGCCAGCTCACGGACAATACGGTAAATCTGCTGTTTGGCTTCGATATCGACGCCGCGCGTTGGCTCGTCGAGCAACAAAATCTGG   >  SRR3722077.975074/1‑100 (MQ=60)
                                                                                             CTTTTCCCTTCGGCAGCCAGCTCACGGACAATACGGTAAAACTGCTGTTTGGCTTCGATATCGACGCCGCGCGTGGGCTCGTCGAGCAACAAAATCTTGC  >  SRR3722077.50611/1‑100 (MQ=60)
                                                                                                  |                                                                                              
TGAAACTCCTGCGAGAACGTGCCGTGCTGTAATAACAGGATGCGGTCACACACCAGCGGCAACTCCTCCACTTCACTGGAGATAAACACCACGCTTTTTCCTTCGGCAGCCAGCTCACGGACAATACGGTAAATCTGCTGTTTGGCTTCGATATCGACGCCGCGCGTTGGCTCGTCGAGCAACAAAATCTGGC  >  NZ_CP009273/2670261‑2670453

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑